Batch effect removal before merging microarray data sets
Hi,
I know that expression data generated by different experiments cannot be combined directly for downstream analysis due to "batch-effects". My question is very straight forward. Is batch effect removal necessary before merging normalized microarray datasets that use the same Affymetrix platform but different chip types, say HG-U133A and HG-U133PLUS2. Or simple merging can solve the purpose?
All kind suggestions will be appreciated.
Thanks
1 answer
boxplot can easily figure out it.
you can use combat (http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html)
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Zhilong Jia
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